Variant report

Variant	rs2267633
Chromosome Location	chr6:29570841-29570842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29567658..29569553-chr6:29570192..29572225,2	K562	blood:
2	chr6:29564780..29575712-chr6:29592511..29597522,14	K562	blood:
3	chr6:29566358..29568865-chr6:29570413..29572313,3	K562	blood:
4	chr6:29566782..29572750-chr6:29592808..29598864,8	K562	blood:

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17508548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2057009	0.97[ASN][1000 genomes]
rs2076483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28359963	0.97[ASN][1000 genomes]
rs28359970	0.96[ASN][1000 genomes]
rs28893513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28986300	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28986304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs29230	0.97[ASN][1000 genomes]
rs29259	0.97[ASN][1000 genomes]
rs29267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41291770	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv528285	chr6:29566842-29588146	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv462671	chr6:29566842-29588146	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv601229	chr6:29566842-29588146	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2267633	HIST1H2BJ	cis	cerebellum	SCAN
rs2267633	HLA-A	cis	multi-tissue	Pritchard
rs2267633	HIST1H1E	cis	parietal	SCAN
rs2267633	GPX6	cis	parietal	SCAN
rs2267633	HCG4	cis	multi-tissue	Pritchard
rs2267633	HLA-H	cis	multi-tissue	Pritchard
rs2267633	HLA-G	cis	multi-tissue	Pritchard
rs2267633	HIST1H2AM	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29561600-29571600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:29561800-29571600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:29561800-29573200	Weak transcription	HSMMtube	muscle
4	chr6:29562000-29571800	Weak transcription	Left Ventricle	heart
5	chr6:29562000-29572600	Weak transcription	Fetal Heart	heart
6	chr6:29565600-29572200	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr6:29566400-29595200	Weak transcription	Right Atrium	heart
8	chr6:29566600-29587000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:29566800-29571400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:29566800-29571800	Strong transcription	Fetal Brain Female	brain
11	chr6:29566800-29572000	Weak transcription	Pancreas	Pancrea
12	chr6:29566800-29572400	Weak transcription	HUVEC	blood vessel
13	chr6:29566800-29584600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:29566800-29590000	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr6:29566800-29590600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:29567000-29571000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:29567000-29571200	Weak transcription	Brain Angular Gyrus	brain
18	chr6:29567000-29571800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr6:29567000-29589800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:29567200-29571800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:29567200-29571800	Weak transcription	Esophagus	oesophagus
22	chr6:29567200-29589400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr6:29567200-29589800	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:29567400-29572000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:29567600-29574600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr6:29567600-29583800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:29567600-29592400	Strong transcription	Fetal Stomach	stomach
28	chr6:29567600-29595400	Weak transcription	A549	lung
29	chr6:29567800-29571600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:29567800-29572000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:29567800-29582800	Strong transcription	Ovary	ovary
32	chr6:29567800-29584600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:29568000-29571600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:29568000-29572200	Weak transcription	Primary T cells from cord blood	blood
35	chr6:29568000-29574600	Weak transcription	HSMM	muscle
36	chr6:29568200-29572000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr6:29568200-29572800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:29568400-29572400	Weak transcription	Dnd41	blood
39	chr6:29568400-29582600	Strong transcription	HMEC	breast
40	chr6:29568400-29583600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:29568600-29595200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr6:29568800-29572200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr6:29568800-29578000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr6:29568800-29583200	Strong transcription	NHEK	skin
45	chr6:29569000-29582600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr6:29569000-29582800	Strong transcription	Osteobl	bone
47	chr6:29569000-29584600	Strong transcription	Spleen	Spleen
48	chr6:29569000-29592400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:29569200-29571000	Strong transcription	NH-A	brain
50	chr6:29569200-29571800	Strong transcription	Brain Anterior Caudate	brain

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